4.9.25035

Actual release:

Update bakta to 1.10.3-5.1-light
Update elgato to 1.20.2
Update fastp to 0.24.0
Update mlst to 2.23.0-2025-02-01
Update amrfinderplus to 4.0.15-2024-12-18.1
Update datasets to 16.38.1
Update panaroo to 1.5.1

4.9.24345

Pre-release with some moderate changes:

• bakta has replaced prokka for genome annotation
  • prokka can still be used by setting params.annotator = prokka
• bbduk has been removed (phix removal doesn't seem to be needed with modern sequencers)
• satisfies vs code nextflow linter (version 1.0.4)
  • includes moving all publishDir to conf/modules.config
• adds meningotype
• updates usage for kleborate (may change serotyping)
• updates usage for kaptive (may change serotyping)
• minor updates to other steps
• moves more processes to dockerhub

4.5.24310

Minor release:

• Update mlst to 2.23.0-2024-11-01
• Update blast to 2.16.0
• Update elgato to 1.20.1
• Update iqtree2 to 2.3.6
• Update datasets to 16.30.0
• Update pbptyper to 2.0.0

4.5.24276

Minor release:

Updates mlst to 2.23.0-2024-10-01

4.5.24250

Minor update

• Update amrfinder to 3.12.8-2024-07-22.1
• Update elgato to 1.19.0
• Update mlst to 2.23.0-2024-09-01

4.5.24219

Minor release:

• update mlst to 2.23.0-2024-08-01
• update spades to 4.0.0
• update datasets to 16.22.1

4.5.24184

Minor "update"

• downgrades iqtree2 back to 2.3.1 because of cloudwatch issues

4.5.240626

Moderate Update:

Container Updates:

• updates iqtree2 to 2.3.4
• updates mlst to 2.23.0-2024-06-01
• updates datasets to 16.15.0
• adds Yersinia to the refs that Grandeur uses for Fastani (version 2024-06-26)

Possibly breaking updates:

• removed flag process and replaced with some groovy functions
  Note: works for me!

4.4.240521

Moderate update

• "under the hood" uses some different channels because sometimes spades doesn't fail, but then also doesn't create a consensus fasta file
• updates panaroo to 1.5.0
• updates iqtree2 to 2.3.1
• updates mlst to 2.23.0-2024-05-01
• updates amrfinder to 3.12.8-2024-05-02.2
• updates datasets to 16.15.0

Of note, according to NCBI announcement https://ncbiinsights.ncbi.nlm.nih.gov/2024/04/22/cleaner-blast-databases-more-accurate-results/, blast databases are getting cleaner. I recommend updating any blast databases for efficiency and accuracy.

4.2.20240425

Moderate release:

• Allows user to use roary for multiple sequence alignment with aligner param (param.aligner = 'panaroo' as default)
• Updates AMRFinder container to 3.12.8-2024-01-31.1_2
• Updates datasets to 16.10.3
• Updates mlst to 2.23.0-2024-04-01
• Updates plasmidfinder to 2.1.6_2024-03-07
• Updates Seqsero2 to 1.3.1
• Updates serotypefinder to 2.0.2